pipelines.chromake.scripts.paths
The paths module of chromake contains functions to identify the inputs and the files generated by the chromake pipeline.
| Name | Description |
|---|---|
| get_all_fastq_related_paths | Get the path to the files generated by the pipeline for the samples of all sequencing and projects. |
| get_sequencing_fastq_related_paths | Get the path to the files generated by the pipeline for the samples of a specific sequencing. |
Get the path to the files generated by the pipeline for the samples of all sequencing and projects.
| Name | Type | Description | Default |
|---|---|---|---|
| cfg | dict | Dict representing the configuration of an analysis with the chromake pipeline. | required |
| mode | str | String representing the files to get. Accepted values are: - sequencing (raw fastq) - multiqc_raw (multiqc report regrouping the fastqc of the raw fastq files) - cutadapt (fastq after adapter trimming) - fastqc_trimmed (fastqc reports after the adapter trimming) - multiqc_trimmed (multiqc report after adapter trimming) - bam (bam files after alignment with bowtie2) - bam_filtered_coord (bam files after filtering the non-standard chromosomes and sorted by coordinate) - bam_filtered_name (bam files after filtering the non-standard chromosomes and sorted by name) - bedgraph (bedGrapg files generated by HOMER for UCSC visualisation) | required |
| Name | Type | Description |
|---|---|---|
| list | A list of file paths. |
Get the path to the files generated by the pipeline for the samples of a specific sequencing.
| Name | Type | Description | Default |
|---|---|---|---|
| cfg | dict | Dict representing the configuration of an analysis with the chromake pipeline. | required |
| sequencing_name | str | String representing the name of the sequencing | required |
| mode | str | String representing the files to get. Accepted values are: - sequencing (raw fastq) - multiqc_raw (multiqc report regrouping the fastqc of the raw fastq files) - cutadapt (fastq after adapter trimming) - fastqc_trimmed (fastqc reports after the adapter trimming) - multiqc_trimmed (multiqc report after adapter trimming) - bam (bam files after alignment with bowtie2) - bam_filtered (bam files after filtering the non-standard chromosomes) - flagstat (output of samtools flagstat on the bam files) - stats (output of samtools stats on the bam files) - multiqc_stats (multiqc on the folder containing the stats output) | required |
| Name | Type | Description |
|---|---|---|
| list | A list of all file paths. |